def _plot_default(self):
# Create the plot
index_mapper = LinearMapper(range=DataRange1D(low=0, high=0.0012))
value_mapper = LinearMapper(range=DataRange1D(low=-0.00025, high=0.00025))
plot = SnippetChannelPlot(history=20,
source=self.channels[self.channel-1],
value_mapper=value_mapper,
index_mapper=index_mapper,
bgcolor='white', padding=[60, 5, 5, 20])
add_default_grids(plot, major_index=1e-3, minor_index=1e-4,
major_value=1e-3, minor_value=1e-4)
# Add the axes labels
axis = PlotAxis(orientation='left', component=plot,
tick_label_formatter=scale_formatter, title='Signal (mV)')
plot.overlays.append(axis)
axis = PlotAxis(orientation='bottom', component=plot,
tick_label_formatter=scale_formatter)
plot.overlays.append(axis)
# Add the tools
zoom = ZoomTool(plot, drag_button=None, axis="value")
plot.overlays.append(zoom)
self.tool = WindowTool(component=plot)
plot.overlays.append(self.tool)
# Whenever we draw a window, the settings should immediately be updated!
self.sync_trait('windows', self.tool)
return plot
def _add_default_axes_and_grids(self, plot, value):
value_trait = self.data.trait(value)
axis = PlotAxis(plot, orientation='left', title=value_trait.label)
plot.overlays.append(axis)
index_title = self.paradigm.get_parameter_label(self.data.parameters[-1])
axis = PlotAxis(plot, orientation='bottom', title=index_title)
plot.overlays.append(axis)
minor, major = value_trait.suggested_grid
add_default_grids(plot, minor_value=minor, major_value=major)
def _update_experiment_plot(self):
index_range = ChannelDataRange(trig_delay=0)
index_range.sources = [self.data.contact_digital]
index_mapper = LinearMapper(range=index_range)
container = OverlayPlotContainer(padding=[20, 20, 50, 5])
self._add_experiment_plots(index_mapper, container)
# Add axes and grids to the first plot
plot = container.components[0]
add_default_grids(plot, minor_index=0.25, major_index=1)
add_time_axis(plot, orientation='top')
self.experiment_plot = container
def _generate_experiment_plot(self):
index_range = ChannelDataRange(trig_delay=0)
index_range.sources = [self.data.spout_TTL]
index_mapper = LinearMapper(range=index_range)
self.index_range = index_range
container = OverlayPlotContainer(padding=[20, 20, 50, 5])
self._add_experiment_plots(index_mapper, container, 0.5)
plot = container.components[0]
add_default_grids(plot, major_index=1, minor_index=0.25)
add_time_axis(plot, orientation='top')
self.experiment_plot = container
def _data_changed(self):
index_range = ChannelDataRange(trig_delay=0)
index_range.add(self.data.spout_TTL)
index_mapper = LinearMapper(range=index_range)
value_range = DataRange1D(low_setting=-0, high_setting=1)
value_mapper = LinearMapper(range=value_range)
container = OverlayPlotContainer(bgcolor='white', fill_padding=True,
padding=50, spacing=50)
# SIGNAL
plot = TTLPlot(source=self.data.signal_TTL,
index_mapper=index_mapper, value_mapper=value_mapper,
fill_color=(0, 1, 0, 0.5), rect_height=0.2, rect_center=0.9)
container.add(plot)
# PUMP
plot = TTLPlot(source=self.data.pump_TTL,
index_mapper=index_mapper, value_mapper=value_mapper,
fill_color=(0, 0, 1, 0.5), rect_height=0.2, rect_center=0.7)
container.add(plot)
# SPOUT
plot = TTLPlot(source=self.data.spout_TTL, reference=0,
index_mapper=index_mapper, value_mapper=value_mapper,
fill_color=(1, 1, 1, 0.5), rect_height=0.2, rect_center=0.5)
container.add(plot)
# OVERRIDE
plot = TTLPlot(source=self.data.override_TTL, reference=0,
index_mapper=index_mapper, value_mapper=value_mapper,
fill_color=(1, 0, 0, 0.5), rect_height=0.2, rect_center=0.3)
container.add(plot)
# FREE RUN
plot = TTLPlot(source=self.data.free_run_TTL, reference=0,
index_mapper=index_mapper, value_mapper=value_mapper,
fill_color=(1, 0, 0, 0.5), rect_height=0.2, rect_center=0.1)
container.add(plot)
# Add the axes and grids
grid = PlotGrid(mapper=plot.index_mapper, component=plot,
orientation='vertical', line_color='lightgray',
line_style='dot', grid_interval=0.25)
plot.underlays.append(grid)
grid = PlotGrid(mapper=plot.index_mapper, component=plot,
orientation='vertical', line_color='lightgray',
line_style='solid', grid_interval=1)
plot.underlays.append(grid)
add_time_axis(plot)
add_default_grids(plot, major_index=1, minor_index=0.25)
# set up microphone plot
value_range = DataRange1D(low_setting=0, high_setting=80)
value_mapper = LinearMapper(range=value_range)
plot = RMSChannelPlot(source=self.data.microphone,
index_mapper=index_mapper, value_mapper=value_mapper,
line_color=(0, 0, 0, 0.25))
self.microphone_plot = plot
container.add(plot)
self.contact_plot = container
def _generate_physiology_plot(self):
# NOTE THAT ORDER IS IMPORTANT. First plots added are at bottom of
# z-stack, so the physiology must be last so it appears on top.
# Padding is in left, right, top, bottom order
container = OverlayPlotContainer(padding=[50, 20, 20, 50])
# Create the index range shared by all the plot components
self.physiology_index_range = ChannelDataRange(span=5, trig_delay=1,
timeseries=self.data.ts, sources=[self.data.processed])
# Create the TTL plot
index_mapper = LinearMapper(range=self.physiology_index_range)
value_mapper = LinearMapper(range=DataRange1D(low=0, high=1))
plot = TTLPlot(source=self.data.sweep,
index_mapper=index_mapper, value_mapper=value_mapper,
reference=0, fill_color=(0.25, 0.41, 0.88, 0.1),
line_color='transparent', rect_center=0.5, rect_height=1.0)
container.add(plot)
# Create the epoch plot
plot = EpochPlot(source=self.data.epoch, marker='diamond',
marker_color=(.5, .5, .5, 1.0), marker_height=0.9,
marker_size=10,
index_mapper=index_mapper, value_mapper=value_mapper)
container.add(plot)
add_default_grids(plot, major_index=1, minor_index=0.25)
# Hack alert. Can we separate this out into a separate function?
if self.parent is not None:
try:
self.parent._add_experiment_plots(index_mapper, container)
except AttributeError:
pass
# Create the neural plots
value_mapper = LinearMapper(range=self.physiology_value_range)
plot = ExtremesMultiChannelPlot(source=self.data.processed,
index_mapper=index_mapper, value_mapper=value_mapper)
self.settings.sync_trait('visible_channels', plot, 'channel_visible', mutual=False)
overlay = ChannelNumberOverlay(plot=plot)
self.sync_trait('show_channel_number', overlay, 'visible')
plot.overlays.append(overlay)
container.add(plot)
add_default_grids(plot, major_index=1, minor_index=0.25,
major_value=1e-3, minor_value=1e-4)
axis = PlotAxis(component=plot, orientation='left',
tick_label_formatter=scale_formatter, title='Volts (mV)')
plot.underlays.append(axis)
add_time_axis(plot, 'bottom', fraction=True)
self.physiology_plot = plot
tool = MultiChannelRangeTool(component=plot)
plot.tools.append(tool)
overlay = SpikeOverlay(plot=plot, spikes=self.data.spikes)
self.sync_trait('visualize_spikes', overlay, 'visible')
plot.overlays.append(overlay)
self.spike_overlay = overlay
# Create the threshold overlay plot
overlay = ThresholdOverlay(plot=plot, visible=False)
self.sync_trait('visualize_thresholds', overlay, 'visible')
self.settings.sync_trait('spike_thresholds', overlay, 'sort_thresholds', mutual=False)
self.settings.sync_trait('spike_signs', overlay, 'sort_signs', mutual=False)
self.sync_trait('channel_sort', overlay, 'sort_channels', mutual=False)
plot.overlays.append(overlay)
self.threshold_overlay = overlay
self.physiology_container = container